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adam

A genomics processing engine and specialized file format built using Apache Avro, Apache Spark and Parquet. Apache 2 licensed.

avocado

A Variant Caller, Distributed. Apache 2 licensed.

bam2fastq

Bam to Fastq processing using Toil

bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

bdg-convert

Conversions to and from Big Data Genomics Avro Formats. Apache 2 licensed.

bdg-convert-ga4gh

Conversions between GA4GH Protobuf and Big Data Genomics Avro Formats. Apache 2 licensed.

bdg-formats

Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed.

bdghbase

bdghbase: an HBase storage backend for Big Data Genomics

biodata

Java library that models biological entities and their equivalents in different file formats typically used in bioinformatics

cannoli

Big Data Genomics ADAM Pipe API wrappers for bioinformatics tools. Apache 2 licensed.

cell-maps

An open-source web-based HTML5 systems biology tool for visualizing and analysing biological networks

cellbase

High-Performance NoSQL database and RESTful web services to access to most relevant biological data

cgl-docker-lib

clone_me

datastore

Datastore library for querying RDBMS and NoSQL databases

eqtl-analysis-using-adam-and-spark

Analysis of genotypes and gene expression phenotype (eQTLs) using ADAM and Spark

eva

European Variation Archive

exac_browser

Browser for ExAC consortium data

fork_me

ga4gh

This repository implements the schemas from GA4GH available at http://ga4gh.org/#/schemas

ga4gh-schemas

Work on data models and APIs for Genomic data.

genome-maps

An open-source high-performance web-based HTML5 genome browser. Genome Maps can easily be customize and allow browsing user data such as BAM and VCF files among other formats.

genomicsdb

GenomicsDB

glnexus

Scalable datastore for population genome sequencing, with on-demand joint genotyping

glow

An open-source toolkit for large-scale genomic analysis

gnomad_browser

tasks for ExAC + gnomad integration pre-ASHG

grpc-maven-helloworld

HelloWorld gRPC using maven

hgvs-eval

automated evaluation suite to assess tools that manipulate HGVS formatted variants

hpg-aligner

HPG Aligner is an ultrafast and highly sensitive Next-Generation Sequencing (NGS) mapper which supoprts both DNA and RNA alignment

hpg-bigdata

This repository implements converters and tools for working with NGS data in HPC or Hadoop cluster